Model Mélange
Physical Models of Peptides and Proteins
In the Model Mélange activity, you will visit four different stations – each featuring a variety of
different physical models of peptides or proteins. The purpose of this activity is two-fold:

to explore levels of protein structure – secondary, tertiary and quaternary structure.
Primary structure will be explored briefly in the context of secondary structure.

to explore different model formats. Each format provides useful, but different,
information regarding the structure.
The worksheets that follow will guide your exploration of each station.
The CPK Color Scheme
The standard colors of different atom types….established by Corey, Pauling (as in Linus) and
Kolton.
Note that hydrogen atoms are typically NOT
displayed in these models. There are two reasons
Carbon is grey (or black)
for this:
Oxygen is red
Nitrogen is blue
Hydrogen is white
Phosphorus is orange
Sulfur is yellow
Zinc is green

X-ray crystallography, which has been
used to determine the structure of many
of the models, does not resolve the
position of hydrogen atoms.
 Because there are so many hydrogen
atoms in many structures, if they were
displayed, most of the rest of the structure
would be obscured.
Station 1: Secondary Structure: α Helices
There are three different depictions of the α helix at this station:
1. α helix construction kit: standard CPK colors, hydrogen bonds are depicted by metal
posts with white balls. The green dots are on the central carbon atom (the α carbon) of
each amino acid. This is the carbon atom to which the sidechain, amino and carboxyl
groups are attached.
2. α helix without sidechains: CPK colors, green dot on α carbon.
3. α helix with sidechains: this is the same model as #2, but the sidechains have been
added. Note that the backbone atoms are colored in light CPK colors (light grey is
carbon, pale blue is nitrogen, pink is oxygen). Sidechains are in normal CPK colors.
Alpha carbon atoms are identified by a green dot.
Use these models to work through the activities below and answer the questions.
1. Identify the amino (N-terminal) and carboxy (C terminal) ends of the α helix.
2. How many amino acids are depicted in this structure?
3. How many hydrogen bonds stabilize this structure?
___
___
4. Numbering of a peptide begins at the N terminus and goes toward the C terminus,
based on the order in which the peptide was made in the cell. Complete the following
statement that describes the hydrogen bonds that stabilize the α helix:
The carbonyl oxygen of amino acid number 1 is hydrogen-bonded to the amino
nitrogen of amino acid number ___.
5. What are the four atoms that make up the repeating structural unit (backbone) of this
model of the α helix?
6. Describe (or draw) the path the backbone takes in 3D space.
7. The pitch of the helix is defined as the number of repeating units per turn. What is the
pitch of the α helix?
8. What feature contributes most to the stability of the α helix?
9. Beginning at the N-terminal end, what is the amino acid sequence of this peptide?
10. Examine the model and predict which “face” of the helix is directed toward the center
of the protein. (Recall that the protein folds in the aqueous environment of the cell.)
List the amino acids on this “face”. Also list the amino acids which are on the “face”
exposed to the outside of the protein.
a. Amino acids directed toward the inside:
b. Amino acids directed toward the outside:
c. What principles of chemistry influenced your selection of these amino acids?
11. If there is time, use the α helix construction kit to build a model helix A of β globin (see
laminated sheet).
12. Summarize what you have learned about α helices.
Station 2: Secondary Structure: β Helices
There are three different depictions of the β sheet at this station:
1. β sheet construction kit: standard CPK colors, hydrogen bonds are depicted by metal
posts with white balls. The yellow dots are on the central carbon atom (the α carbon) of
each amino acid. This is the carbon atom to which the sidechain, amino and carboxyl
groups are attached.
2. β sheet without sidechains: CPK colors, yellow dot on α carbon.
3. β sheet with sidechains: this is the same model as #2, but the sidechains have been
added. Note that the backbone atoms are colored in light CPK colors (light grey is carbon,
pale blue is nitrogen, pink is oxygen). Sidechains are in normal CPK colors. Alpha carbon
atoms are identified by a yellow dot.
Use these models to work through the activities below and answer the questions.
1. Identify the N-terminal and C terminal ends of the peptides that make up this threestranded β sheet.
2. β sheets can be either parallel (all strands running in the same direction from N terminus
to C terminus) or antiparallel (alternating strands are oriented in the opposite direction).
Which type of β sheet is represented in this model?
3. Which type of β sheet could contain a ‘hairpin’ (looped) structure?
4. What role do sidechains play in the hydrogen-bonding that stabilizes protein secondary
structure?
5. How many amino acids are there in the longest β strand in this model? ___
6. Beginning with the N-terminal end of the ‘hairpin’, what is the sequence of the first eight
amino acids of this peptide?
7. What pattern do you notice about the orientation of each successive amino acid sidechain
relative to the plane of the β sheet?
8. How many hydrogen bonds stabilize this structure? ___
9. What are the four atoms that make up the repeating structural unit (backbone) of this
model of the β sheet?
10. Describe (or draw) the path the backbone takes in 3D space.
11. The pitch of the sheet is defined as the number of repeating units per turn. What is the
pitch of the β sheet?
12. Examine the model and predict which “face” of the sheet is directed toward the center of
the protein. (Recall that the protein folds in the aqueous environment of the cell.) List the
amino acids on this “face”. Also list the amino acids which are on the “face” exposed to
the outside of the protein.
a. Amino acids directed toward the inside:
b. Amino acids directed toward the outside:
c. What principles of chemistry influenced your selection of these amino acids?
13. Summarize what you have learned about β sheets.
Station 3: Tertiary Structure: Zinc Fingers
This station focuses on tertiary structure utilizing zinc fingers. Zinc fingers share a common
structure which includes 27 amino acids arranged in a two stranded β sheet and a single α helix.
A zinc atom stabilizes the secondary structure and is coordinated by four amino acids – a
combination of cysteines and histidines. This particular zinc finger has two cysteines and two
histidines. The zinc finger motif is often found in proteins that interact with DNA. [You can see a
zinc finger in association with the DNA in one of the zinc finger models on the stand.]
Perhaps you have heard the story of the seven blind men and the elephant? Each man felt a
different part of the elephant and described it, then argued about which description was right.
Another man resolved the argument by pointing out that each man had only seen a part of the
elephant, and that an elephant included ALL of their descriptions.
Similar to the elephant story, there are several models of zinc fingers at this station. Each
depicts different aspects of the protein. When trying to tell a story about how a protein functions,
scientists determine which features of the protein they want to emphasize, then choose the
depiction that best illustrates those features.
Match each physical model of the zinc finger to the correct format listed below, then list one
positive and one negative feature of that format.
α Carbon Backbone Format
Advantage:
Disadvantage:
All Atoms Backbone Format
Advantage:
Disadvantage:
All Atoms Format
Advantage:
Disadvantage:
Surface Format
Advantage:
Disadvantage:
α Carbon Backbone with Selected Sidechains Format
Advantage:
Disadvantage:
If you only had one model format to use in your classroom, which format would you find most
useful?
Station 4: Quaternary Structure
Some, but not all, proteins contain multiple peptides. This station allows you to explore several
proteins that demonstrate this quaternary structure, as well as a few that lack quaternary structure.
As you explore each of these proteins, see if you can determine:
1.
2.
3.
4.
How many subunits are in the protein?
Based on this information, does the protein have quaternary structure?
Are there α helices in the protein? (If so, how many helices?)
Are there β sheets in the protein? (If so, how many strands?)
Aquaporin
GFP (Green Fluorescent Protein)
Hemoglobin
Beta-Globin
Influenza HA (Hemagglutinin)
MHC (Major Histocompatibility Complex)
F0 complex (from ATP synthase)